TB-Profiler result

Run: SRR28868381
Summary

Run ID: SRR28868381

Sample name:

Date: 2025-02-11T20:16:28.480813

Number of reads: 30314

Percentage reads mapped: 81.83

Median coverage: 1.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.98
lineage4.9 Euro-American (H37Rv-like) None 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 1.0 streptomycin Uncertain significance Mutation from literature
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
rpoB 761615 c.1809A>C synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036A>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 1.0 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 1.0 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 1.0 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.87 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.92 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.91 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.9 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.9 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.9 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.89 rifampicin Not assoc w R - Interim
rpoC 764830 c.1461C>G synonymous_variant 0.88 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 1.0 rifampicin
rpoC 766738 c.3369G>T synonymous_variant 1.0 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 1.0 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 1.0 rifampicin
rpsL 781832 c.273T>C synonymous_variant 0.83 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.86 streptomycin
rpsL 781859 c.300T>C synonymous_variant 0.88 streptomycin Not assoc w R - Interim
rpsL 781868 c.309T>C synonymous_variant 0.88 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.88 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.92 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.92 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.91 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.9 streptomycin Uncertain significance
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.94 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.88 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.93 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.93 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.91 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
rpsA 1833928 c.387G>C synonymous_variant 0.98 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.98 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.98 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.97 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.95 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.93 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.93 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.8 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.8 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.8 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 1.0 pyrazinamide
clpC1 4038701 c.2004G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038707 c.1998C>G synonymous_variant 1.0 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038755 c.1950G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038815 c.1890G>T synonymous_variant 1.0 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 1.0 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 1.0 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 1.0 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 1.0 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 1.0 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim